- Automatically find broken links on GN2
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 2 of 2 tasks done
...broken links
### Notes
the bug above no longer exists.
gn2 CI runs on the background after for any push
raises an error if any broken link is found
On gn2 web pages all missing links that are found...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...is broken. An exception stack trace is displayed, instead of the annotations page content.
## Info
Lily runs a PHP from 2006(!)
PHP 5.1.6 (cli) (built: Mar 18 2014 20:48:55)
Copyright (c) 1997-2006...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR Version.
The root cause of the problem is unclear,
but after reviewing...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
.../421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID=annotation The annotations page in GN1
is broken. An exception stack trace is displayed, instead of the annotations page content.
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...an issue tracker on gemini
Why do we want to consolidate issue trackers and kanban boards using gemini+git? Several reasons:
* Get rid of external web service dependencies (in our case github issue...
- GN1 Production
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
...tmp dirs with CRON
=> gn1-mapping-broken.gmi [ ] Marker regression is broken
* [ ] Fix annotation link - appears to be a hard coded redirect
* [ ] Enable time machines
* [ ] Disable all defunct URLs...
- Each shepherd service needs its own guix profile.
issue opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
...migrated:
* covid19-pubseq (uses shared (broken!) guix profile, uses shared config directory)(currently running by hand by Pjotr)
* hrdp-project (uses shared (broken!) guix profile) (upstream source...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...issue
- [X] Check if database is affected in any way
- [X] Send a patch to fix
- [X] Notify every relevant user
- [X] Update case-attr page with links
## Notes
### Mon 11 Apr 2022 13:19:14 EAT:
The...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...The idea is to add a new track to mouse/rat mapping figures that provides links to the corresponding region for humans in the UCSC Genome Browser.
This can be done using these UCSC chain files. Links...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...tabular form and too many columns are presented to user overlapping the page
Design should be simple and eye catching to user
links to suggesetd designs:
=> https://www.ncbi.nlm.nih.gov/genome/?term...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...the mappings of individuals to strains exists in the CaseAttributes tables. A Temp trait could be created for the purposes of the analysis (though this presents potential issues with trait page links).
- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...and some are broken.
We found out that there are quite a full network calls using DNS - and DNS was slow. The configured DNS server was not responding. Using Google's DNS made things go fast again.
- Fallback issues
issue opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done
...has links to
=> https://d3js.org/d3.v7.js
=> https://d3js.org/d3.v7.min.js
We can't use those because the SHA may change. So we have to host a local copy. That is fine.
## 413 Request Entity Too Large...
- GN Markdown Editor Integration
issue opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done
...APIs to fetch files for editing
* [x] Add verification for the repository
* [x] Implement API to edit and commit changes
* [x] Replace JS with HTMX
* [x] Support external links and image rendering...
- Add an 'Edit Issue' Link to Tissue
✓ issue opened on Mar 24 2022 by Frederick Muriuki Muriithi, last updated on Apr 15 2022 by Arun Isaac
...tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub) editting mode for the selected file.
For an example of what is expected...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...trait_id=1448231_at&dataset=HC_M2_0606_P
>
> jacs123
I (fredm) tried this out, and it seems there is still an issue here.
This appears to no longer be an issue; it was probably addressed along...
- Investigate and Fix `rm` Command in `rqtl` Logs
issue opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done
...the observed issue.
## TODO
* [ ] Test in a similar environment to the CD environment to replicate the issue.
* [ ] Investigate the internals of the QTL library for any unintended `rm` invocation.
- 'TempDataSet' object has no attribute 'query_for_group' (error)
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Sep 28 2022 by Alexander_Kabui
...might also be interested in this issue
## Notes 28/9/22
this issue has not being reported for a while since jul 16,2021
The error is also not reproducible
closing down this until a new issue is raised
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...identify
the file in the GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to:
=> https://github.com/genenetwork/genenetwork3/blob/main/gn3/db/genotypes.py
* Linked to issue...
- Zoomed mapping result are empty for certain traits
issue opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
...issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed first in the GEMMA results for a later chromosome.
For example...
- Global search does not close connections properly (and is slow)
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
...of log file info.
In fact, every row in the table has a SQL query that does not close the connection properly.
## Resolution
The new xapian search does not use the SQL database at all. Therefore issue...
- correlation error: 'NoneType' object is not iterable
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 13 2022 by Alexander Kabui
.../wqflask/wqflask/correlation/show_corr_results.py", line 473, in process_samples
for sample in sample_names:
```
## notes
codebase for gn2 correlation had a rewrite
and this is no longer an issue
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...API - so people van validate client side (as a feature).
This mentions RDF - which I think
* aruni
was involved in. I (fredm) have tagged them here, for their evaluation of the relevance of this issue...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...This issue addresses user feedback received during the testing phase of GNQA on CD. The following improvements are required
## Tasks
* [ ] Only show the link when a user is logged in - they can't use...
- Capture Data on the BXDs in RDF
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...dumping RDF has already been done in:
=> https://github.com/genenetwork/dump-genenetwork-database dump-genenetwork-database
Also, vector/matrix data should be put in lmdb, and this is a separate issue...
- GN2 Time Machines
issue opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done
...wrong.
Use the console bar of the browse to see what JS error you get.
If you get CORS errors it is because you are using a server that is not genenetwork.org and this is usually a configuration issue.